From both EWR and JFK I would strongly recommend the train as outlined in earlier posts.

I made the mistake to take an Uber from JFK to Manhattan (next to Penn) and paid $85 and the journey took 1,5 hours (around lunch time so off peak). AirTrain and LIRR is much faster and convenient / safe.

Same applies for the EWR train to Penn, even easier.

Edit: Download the MTA app on the UK app store and you don't have to bother with train tickets plus you see departure times (works w/ UK credit cards).