Of the two, IMO Secret Harbour is hands down the better choice. Also have you considered renting a private condo from the owner. VRBO.com or Homeaway.com have a lot of condos for rent directly from the owners. The prices are usually lower than going through a management company such as that used at the two places you mentioned, and the prices are always lower than the price of 2 hotel rooms. On VRBO.com under St. Thomas, look at the condos listed under Cowpet Bay, Sapphire Beach and Point Pleasant. Good luck.
I agree with BruSue - Secret Harbour would be my choice by a mile (I have stayed at both). The beach at Secret Harbour is much nicer than the beach at Bolongo, and I strongly prefer the overall atmosphere at Secret Harbour.
Slam Dunk Secret Harbour. The beach is much nicer and you are in close proximity to a lot more restaurants and activities. Plus I swear the no see-ums are the sixe of cats at Bolongo, just downright mean.
Another vote for Secret Harbour. Nice beach, great location, excellent restaurant. Bolongo Bay does have Iggy's, which can be fun for their West Indian show (if they still do that one night during the week), but you can go to that on your own.