The best way is by using the wall charger that came with it - you may also be able to charge it by connecting it to a computer's USB port, but a lot of computers don't provide much power to their USB ports, so generally that will be slower than with the wall charger : charging an iPad.
You should also go through regular charge cycles - from here :
For proper reporting of the battery’s state of charge, be sure to go through at least one charge cycle per month (charging the battery to 100% and then completely running it down).
The quickest way (and really the only way) to charge your iPad is with the included 10W or 12W (5W on Mini) USB Power Adapter. iPad will also charge, although more slowly, when attached to a computer with a high-power USB port (many recent Mac computers) or with an iPhone Power Adapter (5W). When attached to a computer via a standard USB port (2.5W, most PCs or older Mac computers) iPad will charge very slowly (but iPad indicates not charging). Make sure your computer is on while charging iPad via USB. If iPad is connected to a computer that’s turned off or is in sleep or standby mode, the iPad battery will continue to drain.
Apple recommends that once a month you let the iPad fully discharge & then recharge to 100%.
How to Calibrate Your Mac, iPhone, or iPad Battery
At this link http://www.tomshardware.com/reviews/galaxy-tab-android-tablet,3014-11.html , tests show that the iPad 2 battery (25 watt-hours) will charge to 90% in 3 hours 1 minute. It will charge to 100% in 4 hours 2 minutes. The new iPad has a larger capacity battery (42 watt-hours), so using the 10W charger will obviously take longer. If you are using your iPad while charging, it will take even longer. It's best to turn your new iPad OFF and charge over night. Also look at The iPad's charging challenge explained http://www.macworld.com/article/1150356/ipadcharging.html
Also, if you have a 3rd generation iPad, look at
Apple: iPad Battery Nothing to Get Charged Up About
Apple Explains New iPad's Continued Charging Beyond 100% Battery Level
New iPad Takes Much Longer to Charge Than iPad 2
Apple Batteries - iPad http://www.apple.com/batteries/ipad.html
Extend iPad Battery Life (Look at pjl123 comment)
New iPad Slow to Recharge, Barely Charges During Use
Best Practices for iPad Battery Charging
Tips About Charging for New iPad 3
How to Save and Prolong the battery life of your new ipad
Prolong battery lifespan for iPad / iPad 2 / iPad 3: charging tips
iPhone, iPod, Using the iPad Charger
Install and use Battery Doctor HD
To Extend a Device’s Battery Life, Get to Know It Better
iPad Battery Replacement
In rare instances when using the Camera Connection Kit, you may notice that iPad does not charge after using the Camera Connection Kit. Disconnecting and reconnecting the iPad from the charger will resolve this issue.
You charger will get warm when charging your iPad. Whether or not one considered that hot is hard to say. If you feel your charger is too hot make an appointment at an Apple store to have it looked at just to make sure.
You can charge the battery in an iPad at any time. You do not have to wait until it is near or at zero. You can leave it on the charger after it reaches 100% and this will cause no problems.
You can stop charging it before it reaches 100 as well with no problems resulting.
Apple recommends a complete discharge once a month in order to recalibrate the software that tracts the level of the battery. I've never found that necessary though. If I notice that my iPad doesn't quite make it to 100% I reset my iPad and that corrects that problem.
To reset your device. Press and hold the Home and Sleep buttons simultaneously ignoring the red slider should one appear until the Apple logo appears. Let go of the buttons and let the device restart.
I have the same problem as yours. i bought ipad Mini and discovered my iPad Mini will stop charging at 90% or 65% or 70% once the supplied USB adapter gets TOO HOT...i suspect the USB adapters is faulty because i have no problem when i am using my Iphone 4 USB adapters. i can charge my Ipad Mini up to 100% with ease and the adapter is not as HOT compared to ipad Mini Usb Adapter. i need to wait for the ipad Mini USB adapter to cool down before it starts to charge up again. This is very troublesome because we have no idea when the charging will stop at certain percentage.
I also noticed the difference between ipad mini USB adapter and iphone 4 USB adapter. Ipad Mini USB adapter is manufactured by Salcomp (Shenzhen) Co. Ltd while the Iphone 4 usb adapter is manufactured by Emerson Network Power. I have NO problem charging my ipad mini to its full capacity (100%) when using iphone 4 Usb adapter by Emerson Network Power. (Please refer to attached pictures).
I went to Apple Reseller store and they all aware of the problems & a lot of the customers complains... But they could not change a New USB adapter for me. They asked me to refer directly to apple care by calling their toll free no.
Picture No.1 - IPAD MINI usb Adapter - Salcomp (Shenzhen) Co. Ltd.
Note: Charge up to 90% or less, adapter can gets very HOT while charging.
Picture NO.2. - Iphone 4 USB Adapter - EMERSON NETWORK POWER
Note: No problem charging Ipad Mini. Can charge up to 100% with ease. Adapter is warm and NOT Hot while charging.