Kim...
We've done San Juan as pre and post tortola several times. Have looked for the most reasonable three star in the isla verde area. Hojo, holiday inn, ramada, etc. Not looking for amenities when you are just crashing for a night and early out next day. Kayak or hotels.com are good shopping sites.
A night in old SJU is good for a nice dinner...especially for any crew that hasn't been there before. If you have extra time, suggest a 1 or 2 hr tour from down town near the cruise terminal.
If all of you flying together, a charter non stop to VG may be worthwhile. I haven't seen Bill H on the board lately.