moving to AWS RDS (InnoDB vs MyISAM
Without knowing your dataset size, or your usage (read or write heavy? queries per second?), here are some generalities:


InnoDB has improved drastically in even the last few years performance-wise. This, along with the (mostly) ACID compliance and row-level locking, is why it's now the default in 5.5+
If you're not using full text indexes in your MyISAM table, you should be fine switching to InnoDB
Make sure you know the changes to the mysql version you're going to on RDS. Performance might not be the only 'gotcha' on moving to InnoDB at RDS. If RDS is newer than your current application, make sure there's not any features that changed. You do this by:
Test it!! Don't make the move on your application until you've tested it out. 




One method to test it is to turn on the general query log for a week or so (if the performance hit won't be an issue) and then run it against the RDS instance to see how it runs.

Disclaimer: I'm not an expert on RDS, so I don't know the best way to test against it.