My gf and I had a great time while on NY. We booked Wendy's apt for 9 nights, it was really easy to arrive eventhough we landed at Newark Int Airport (obviously it took a while, but really straight forward). The C line metro station is 8ish minutes away (walking). Late nights (midnight to 6am C doesnt run, so A line makes all the same stops as C, while in regular hrs A is an express Line). Lots of times we took A to Novstrad (express) and then C line to Kingston just to get home faster. Novstrad is not that far way fromt he apt tho, it is a 15-20min walk. Last day we were there C line was on maintenance and Kingston Station was closed, so we had to walk down to Novstrad, it wasnt that long of a walk.
Most of the time we would leave the apt at 5ish am and come back at 11ish pm. While walking through the streets on that darkness no one messed up with us or tried anything funny, if anything, people say "sorry" if accidentally bumped you while walking, which is nice and respectful.
The apt is super clean, and had all we the tools we needed to cook. Wendy came around to say "hi" and was very friendly. We def loved the place.
The advantages of the location is that we could get to Penn Station really easy, and from there branch out to any place. Also, Kingston Station is close to a shuttle that takes you to the B,Q lines that can take you to Coney Island to the Park or beach, which what we did.