Probably depends on where in the city you are going.

I prefer EWR, but usually travel with little baggage, and find the airtrain/NJ Transit option into Penn station by far the easiest way into the city. Amtrak is available too, but probably about double to triple the cost, with not much faster of a travel time. If you time it right, you can be from the terminal to the city in 30-40 minutes. But if you're going to Long Island, Queens, etc, its a pain and takes much longer.

LGA ground transfers are all on road, and you're at the mercy of NYC traffic, so you really never know how long the trip will take.

In terms of facilities, Terminal A at EWR and the LGA facilities are probably equally as poor.