There's a "basic" hotel right in the San Juan Airport - nothing fancy but clean & comfortable - above all very convenient.

Otherwise look at the following (all within a 10 minute or so drive):

Rotz Carlton
El San Juan
Intercontinental
Embassy Suites
Hampton Inn & Suites
Holiday Inn Express

It's always difficult to predict how long it will take to get through the TSA check point at any given airport on any given day. I can tell you this the TSA lines at SJU move very S-L-O-W no matter what day or time. If I were you I'd allow at least 30 minute to get through the TSA checkpoint - if you are lucky and take less time all well and good, if they move at there usual pace you won't feel rushed.

If your flight's at 6AM I'd arrive at the airport no later than 4:30AM if you have to check-in and get your boarding passes - if you've checked-in online and already have your boarding passes get to the airport no later than 5:00AM for a 6:00AM flight. It's ALWAYS better to wait by the gate for a few extra minutes rather than risk missing your flight while you are "stuck" in a slow moving TSA line.

and don't forget that you have to pass a separate agriculture checkpoint with all of your luggage - luggage you are checking, and everything that you are carrying on except your purse -- before you get to the counter to even check in for your flight. The problem is that the last time we were there (a few weeks ago), the USDA checkpoint didn't even open until after 5:30, so there was a big line of people starting at about 5 AM waiting for them to start staffing that line. The USDA checkpoint in the other terminal (the one with JetBlue) might open earlier if they know they have a 6 am flight (the first flight in our terminal was at about 7 am).

But it only takes about 20 minutes to get to the airport (especially at that time of morning - no traffic), so if it were me I would probably still get a hotel in Old San Juan so I could have fun the night before.

Thank you for the advice.
LinB

Carry-on goes through agriculture check too? Thank you Tejana, I thought only my suitcase - glad I looked here.