Seems like you have things pretty well in hand. The wildcard is that there has been a lot of weekend track work affecting the A and E lately, so just because your hotel is served by a train on Friday doesn't mean it will be on Saturday. In particular, the A sometimes operates over the F, the E sometimes operates over 6 Av, the Queens Blvd line is often backed up, etc.

All other things being equal, of the BB and DT I'd pick the BB because Jay St is more likely to have direct airport service, and in a pinch you could go to Atlantic Av for the LIRR to Jamaica.

Alternately, stay near Penn Station. The new Ren usually has slightly better than average rates for the Manhattan properties.