Canon 60 PC Adobe Premiere and After Effects Workflow
I've never noticed any codecs that run smoother in After Effects or Premiere. One thing I have noticed about Premiere is that if you don't have your source media in your main project folder (designated when you start the project), it lags. I assume the RAM gets overly taxed by searching all over the place to round up the referenced files. I haven't seen any documentation about this but have run extensive tests to prove it. I migrated recently from FCP. 

Based on what you said, it sounds like you want to compress your footage before working with it in AE or Premiere. I think this is a bad idea. Your camera has already compressed it (using the h.264 codec). If you absolutely have to use another codec, I would go with:

quicktime animation
quicktime jpeg2000

They are uncompressed or the least compressed to my knowledge. 

As I'm sure you know, when working with AE and Premiere, you want your raw material to be the highest quality possible and only compress it when you export your final project. For example you want to use AIFF (or something comparable) and not mp3 for audio. If you compress it before working with it in AE or PRE and then export it, you're compressing it twice and throwing away data twice. This will kill your quality. 

Another factor may be your memory settings in the apps preferences.

Another possibility, if you're using an external scratch disk, make sure it's not USB. This will cause lag.

Finally, your graphics card and RAM need to be pretty hefty for a pleasant experience.

I run an imac with a 2.8 GHz Intel Core i7 with 16 GB of RAM and a great ATI Radeon HD 4850 512 MB graphics card. It pretty much flies with any codec I use.