Last year I was the National Park's Bay Host at Leinster Bay for about 5 months until the end of the season in early July. We were "required" to take a two day break every week and I made many two day runs about the area both in and around the BVI and other locations on St. John and St. Thomas.
btrayfors was dead on when he indicated a run from most areas on St. Thomas to Leinster Bay with an afternoon start time can be a hard run at times and even in good times, you will not have much time at Leinster / Waterlemon Cay which is a destination
not to be missed. This has some of the best snorkeling and hiking in the islands. Don't miss the old Danish Guard house above the bay which has killer views of the bay... best between 9AM and 11:30 and you will see colorations you will not believe, go on up the trail to Windy Hill for an even better view. Note the fee in the National park is $15.00 per night... a good deal and if you have the Golden Age Pass, think that is still 62+ the fee is $7.50 per night which beats the $25 and $30+ fees
over night in the BVI.
I would check in at West End unless you intend on going to Jost Van Dyke first then just do it. You will have marginally higher fees
on the weekend but not a major thing.
Direction should be governed on the winds and seas. If a strong North Swell is in work, Probably not a problem that time of year, you may want to stick to the Sir Francis Drake Channel for a while.
If you are heading to Anegada from Jost you need to head
out early as you need good light to see the coral
heads and find you way into the channel. I've done it several times and not a problem on a bright day but if overcast it could cause more problems. If Northern Swells are acting up... you will want to avoid Cain Garden Bay and possibly the trip to Anegada unless your crew likes to rock and roll a LOT. Swells should not be a major problem in June but they do occur.
Have fun... I'll be heading back from St. Maarten in late June or early July.
I would also recommend a possible stop at Christmas Cove