I have experience both airports multiple times. My preference is LGA. Here’s my comparison for a trip to mid-town / Chelesa Manhattan:
LaGuardia Airport (LGA)
Hop the free shuttle bus (every 10 min) to the Jackson Av. subway station where multiple subway lines are available. Pay $3.00 and take the line nearest to your destination. Peak times subways generally come every 5 min or less.
Time: about 45 min to one hour.
Pros: Cheap and fast
Cons: Depending at time of day, Shuttle and subway might be crowded.
Visit the official LGA transportation page
Newark Airport (EWR)
Get on the really s-l-o-w airport tram to the airport train station.
Buy the $15 ticket for the NJ Transit train.
Peak times, trains come every 20 – 30 min.
At Penn station, walk to your hotel, or if it is a distance, subway, Uber or Taxi.
Alternate: There is a bus to the Port Authority Terminal on 42 st. However, tunnel traffic is a crap shoot.
Total time – Depends on train frequency – 1 – 1.5 hours.
Pros: Train to NY is a bit more comfortable than the subway
Cons: More connections, more waiting time for trains.
Visit the official Newark Airport transportation page