For simple matters of geography, barring a major accident on the GCP or other adjacent roads, La Guardia will offer the quickest trip by car into any part of Manhattan among the three main commercial airports. (Teterboro probably beats it for uptown destinations, but TEB has no commercial service).
Terminal A (a.k.a. the Marine Air Terminal) is particularly convenient, as it is on the far western edge of the airport, and has a simple layout, and is smaller, making it easier to navigate once off the plane, faster to get a cab at the taxi stand, and quicker to get onto the BQE, thence to the bridge (or, I suppose, the tunnel, but my cabbies always seem to prefer the bridge). In fact, back when the terminal was used by the shuttles, Pan Am and then Delta used its convenience as a selling point.
- It looks like as of writing JetBlue and Alaska use Terminal A. Reference
Yes, LGA is totally chaotic with the massive construction going on. I think, however, that this only makes JFK and EWR more competitive, not clear winners in either case. LGA is simply geographically closest to Manhattan, and thus offers the least uncertainty. With EWR you have the risk of tunnel traffic, which can add an hour if you arrive at the wrong time of day. JFK is on the far side of Queens and almost necessitates time on the Van Wyck.