We've just come back from a trip to California and Vegas. Highly recommend signing up to touringplans.com to pick your best days for Disneyland and Universal Studios. Also highly recommend doing the Warner Bros studio tour!
We didn't go to any collectable stores in LA but went to a few in Vegas. I found the stock to be bit too expensive for what the Australian dollar can buy nowadays, better to simply buy off eBay etc.
For New York, there is a massive TRU in Times Square worth checking out. Also go visit Midtown Comics!
http://www.midtowncomics.com/