I rented out of Grey Eagle a little bit (very small 141 school), and enjoy their rental rates and small school atmosphere. Pinnacle appears to be the biggest school there, with a lot of foreign pilot-mill type students. It looks like ATP is also there, as is "Pacific Coast Flyers" (which is actually a flying club based from multiple airports around San Diego, but they match new student members with a list of approved instructors there). Most of the CRQ real estate is taken up by ludicrously huge corporate jet oriented FBOs though, including Premier Jet and Jetsource which are both VERY nice facilities. (And of course the terminal which
Autothrust Blue briefly sees on the way to his luxurious hotel layovers

).
One last thing to consider is the local weather. Being on the coast, CRQ is often frustratingly socked in by the marine layer while airports further inland like Gillespie are CAVU. Worth considering since the drive really isn't bad at all. MYF is sort of in between.