We've chartered twice in the BVI and 8 times in the USVI over the past dozen years. There are 3 reasons we've chartered out of the USVI for the past 6 years straight:
1. You can get to St. Thomas on a "real" airplane (no need for a puddle jumper) and you avoid the possibility of missing the last ferry from St. Thomas to Tortola if your plane is late.
2. The USVI has some really nice, QUIET bays with extensive hiking trails and with Park Service moorings at $15/night on St. John.
3. Our preferred charter operation is family-run Island Yachts in Red Hook. Their Island Packet Yachts are a cut above the Beneteaus and Jenneaus IMHO. Also, Red Hook has services (grocery, liquor, restaurants, dive shop, pharmacy, Subway, etc.) literally at the Yacht Harbor.
There is a downside to chartering out of the USVI, which is the necessity of customs/immigration stops if you go to the BVI--which you should, especially if you haven't been to the Virgin Islands before. You don't check out of the USVI, but you do check in (and out at the same time) in the BVI at either Jost van Dyke, Sopers Hole (West End), Road Town, or even Spanish Town). You also must check back into the USVI at Cruz Bay if you are going back to Red Hook). The BVI check in/out process is a minor inconvenience, but can take an hour or two, including boat handling. The USVI check in is quick, but typically involves mooring in Caneel Bay and taking your dinghy into Cruz Bay.
A couple of other points: If you've seen the BVI, you can stay with the USVI and avoid the customs scene altogether. St. John, which is mostly a national park, provides excellent snorkeling and--compared to the BVI--relative peace and quiet. Also, we're comfortable with the Island Packets, particularly when the wind picks up, but they are relatively heavy and are not likely to be mistaken for racing boats. Another option out of the USVI is the Spanish Virgins.