Aperture cannot be copied - you need to run an installer. Use your installation DVD to install it on your new iMac; then immediately after installation run "Software Update" from the Apple Menu to update to the latest version. You will have to enter your registration number, it is in the box with the installation DVD. You can also copy the Registration code from your MBP - from Aperture's "About" panel: Aperture menu > About Aperture.
Do you still have the installation media? If not, download the Trial version:
When installing from the DVD you may get an erroro message "Certificate expired". In that case simply change the date of your Mac (in the System Preferences > Date & Time) to a date before February 2012 while you are installing. You can setit back to the correct data later.
Migration Assistant will work fine. Though, keep in mind that you can't just copy over Aperture and it's supporting files ... it's an all or nothing transfer of your Apps, user folder, etc. ... which is quite nice to bring a new computer up to speed very quickly and easily ... too bad that Apple doesn't allow cusromization of what you can migrate ...
While migration assistant should work pro apps like Aperture should be installed for their original install media as per Apple.
Note in either case you will need the original serial number if your version of Aperture was originally purchased on DVD or was a download from the Apple site.
If you use migration assistant to copy over Aperture and the app has problems then do the install from the original media.
What about Migration Assistant?
Setup Assistant is better than Migration Assistant the first Setup, when you are unboxing your new Mac and do the initial setup by copying files from another Mac or a TimeMachine backup. Running Migration Assistant later will not copy all Library items and additional system files like the Setup Assistant does. If you missed to copy Aperture with the original setup it would be safer to reinstall from your installation media or using the Trial installer. But even using Setup Assistant you will have to enter the Serial number. That will not be migrated by Migration Assistant.