I have never stayed at the Marriott Courtyard buy have stayed at the El San Juan several times and the Ritz once. The Ritz is very nice as far as San Juan resorts go and I would stay there every time I was down if the rooms weren't so expensive. I would think it is worth looking into during the time you are going to be down there to see what the rates are. If it is during off season you never know...
The El San Juan is a fun hotel too. Maybe a small step down from the Ritz, but it has a really cool vibe IMO. Nice pool area, great lobby and plenty of good restaurants to choose from, but so-so rooms (though I hear they are remodeling them).
One thing I always do is book an acceptable room at an acceptable hotel at a refundable rate and then keep my eyes on the rates for it as well as other hotels. Most hotels allow you to cancel up to 72 hours before your arrival. So, maybe book at the Marriott if you are happy with the rate and check the rates at the El San Juan and Ritz every now and then. Maybe you'll luck out and get a great rate at a top tier resort.
Matt