I just returned from a NYC trip and flew to/from LGA for the first time. I usually travel in and out of EWR. LGA is such a complete dump, especially Terminal B.

I used public transportation both ways, the Q70LTD bus to the 7 train at Jackson Heights. It was certainly a bargain, since I bought a weekly Metro ticket at the machine (inside) by the bus stop, making the route from/to LGA "free." This transport is only OK if you can carry your luggage up and down multiple flights of stairs. There is an elevator at the Jackson Heights station, but it could be non-functional when you travel.

I much prefer the Olympic Trails bus from/to EWR. That bus has 3 stops in Manhattan: Grand Central, Bryant Park, and Penn Station. No flights of stairs, much less hassle.

Truth be told, none of the NYC airports are "nice," choose based on the best airfare you can get.