If you're looking at flights still and don't know which airport to choose, I'd say book whichever flight is more convenient based on timing and airfare and don't worry about the airport issue too much. Laguardia is a few miles closer to us than JFK is, but it's not a huge difference.
For anybody arriving at either airport, your best transportation option to campus is taxi. (The public transportation option from Laguardia is possible, but it will take at least 2 hours -- take the M60 bus into Manhattan, then the 6 subway uptown into the Bronx, then the Bx40 to campus.)
If you plan to take a cab to campus, take these directions (both options!) with you:
Via the Whitestone Bridge: Pay toll at extreme right booth, take immediate right exit to traffic light. Turn right to next traffic light, turn right then left onto I-295. Keep to right and take EXIT 9 (Harding Ave/Fort Schuyler) just before Throgs Neck Bridge. At EXIT 9 (Harding Ave/Fort Schuyler) go left at stop sign at end of exit ramp, then make immediate right on to Harding Avenue. At stop sign, turn left onto Pennyfield Avenue, and proceed to the end until you reach the Maritime College gatehouse.
OR
Via the Throgs Neck Bridge: Pay toll at extreme right booth, take immediate exit for Pennyfield Avenue-Fort Schuyler. Proceed along service road to 2nd stop sign (2 blocks). Make left onto overpass. At light, veer left onto Pennyfield Avenue, proceed to the end until you reach the Maritime College gatehouse.
My experience has been that cab drivers prefer to take the Whitestone. The bridges cost the same, and they’re about equidistant – I have no personal preference which bridge they use. The only difference will depend on traffic that day, which your cab driver may know about.
We will be including some version of this in your conference packet, which you can use to get back to the airport. The cost to get here from the airport will probably be somewhat less than what it will cost to get to the airport – the yellow cabs are metered, but these local companies go by flat rate. You might be able to carpool with somebody else from the conference; I've communicated this information to two people already. Email me if you would like to get in touch with them about sharing a taxi to the airport after the conference.