Currently, the Westin ferry costs $120 for adults and $90 for children. There are many discussions on the pluses and negatives of using the ferry. It pretty much comes down to personal preference and budget.
IMO, nothing beats the "first impression" of taking the Westin ferry if you're traveling to St. John for the first time. After being awake since 3am, it was a delight to arrive at the airport, and just roll my bags over to the Westin desk. They took care of all logistics up until we stepped into our villa several hours later.
IIRC, we arrived too late for the 11am ferry, but it worked out to our advantage because we discovered "Tickles" at Crown Bay marina, a great al fresco, moderately priced bar/restaurant. So we got to enjoy lunch and some cocktails before catching the 1:45pm ferry. (Hint: get in line early because outside seating is very limited.) We really enjoyed the 45 minute boat ride over to St. John and saw a ton of rainbows. They arrived right at the Westin dock. A short walk later, we were handed cocktails and our room keys by an attendant. No waiting required! "Iguana" (golf cart) drivers were all lined up and ready and waiting to take us and our luggage to our villa. I can't tell you how delightful it was to have this great first impression, especially since we'd be traveling for 12 hours by that time.
Of course, we were lucky enough that the stars were all aligned, and our flights matched up well with ferry schedules.
Current departure times of the WSJ ferry are listed below, and you are correct that they are very limited. But before you dismiss it based on that, know that the Westin will arrange transportation on a private ferry to St. John day or night should you arrive outside of the ferry operation hours. If I were scheduled to arrive in the evening, I'd strongly consider getting the Westin ferry, just in case my flight was delayed (Can you imagine finally arriving at 1am and having to pay to get a hotel room on St. Thomas because you can't get to your villa on St. John?) And, frankly, Red Hook gets a little seedy past dark. Been there, done that.
However, note that there is only ONE morning option now back to St. Thomas, and that is 10am. A 10am ferry to Crown Bay (note that it doesn't go to Red Hook anymore) will get you to the airport ~11am, which is a tad too late for a 1pm flight, perfect for a 2pm flight, and a waste of time for a 3pm or later flight. And with the mandatory 3 hour window that they advise to get through Customs/TSA, anyone that flies out from 2-4:30 should be booked on that 10am ferry, because 12:45pm ferry won't get them to the airport on time. IOW, that 10am ferry is going to be packed, and not necessarily convenient for your specific flight times.
By contrast, the "public" ferry runs hourly (see times below), so many more options. But you're going to have to haul your luggage yourself and pay for taxis from the airport to Red Hook, and from Cruz Bay to WSJ. If you choose this path, know that your first impression will be greatly diminished, but much, much cheaper, and possibly much quicker. So come with an open mind and plenty of cash! Some other upsides: Taking the public ferry also gives you the ability to stop and do some grocery shopping at a "reasonably" priced grocery store on St. Thomas before departing for St. John, where prices are jaw-dropping.
FERRY DEPARTURE TIMES: ALL DAYS OF THE WEEK
DEPART WESTIN DEPART CROWN BAY MARINA
6:00 AM ------------------------
7:00 AM ------------------------
9:00 AM 10:00 AM
11:00 AM 12:45 PM
1:45 PM* 3:00 PM
---------- 5:30 PM*
Another option which is rarely discussed is the ferry from Charlotte Amalie Ferry Dock to Cruz Bay. At $13pp, this may be your best option if your schedule aligns with the limited ferry schedule, because I assume you won't have to pay for a long taxi ride:
40 Min Travel Time
Charlotte Amalie → Cruz Bay
10:00 am
1:00 pm
5:30 pm
Cruz Bay → Charlotte Amalie
8:45 am
11:15 am
3:45 pm
BTW, here are the ferry schedules:
http://www.vinow.com/travel/virgin-islands-ferry-schedules/
Here is a very nice write-up of your options.
http://www.vinow.com/stjohn/getting_there/