Why are you "surprised" that the subway would be safe? It's not as though the New York City subway system was used predominantly to ferry dangerous convicted criminals back and forth or something. The vast majority of riders of the NY subway system are plain, ordinary people, who are just trying to get to where they are going, with no more malice in their hearts than you or me. These are the same people who you find at airports, malls and other public places. Unless you're going to tell me that you have some sort of aversion to any public place where such people might congregate, I don't understand why you would assume anything different about the subways. On what basis are you concluding that the bus from EWR would be "safer still"? Once again, we're talking about the middle of the day on a Sunday.

As far as comfort is concerned, if getting a cushioned seat is a priority, you can always take the LIRR from JFK; IMO, their seats are more comfortable than the airport bus seats. More importantly though, I think the biggest comfort that you can enjoy when coming into Manhattan from any of the three airports is getting to your destination as quickly as possible. While it may be possible to get from EWR to the upper east side faster than from JFK or LGA, I would guess it's more the exception than the rule. The day that this particular visitor is coming in is the Sunday before Xmas. Traffic is going to be a madhouse, all over Manhattan, and particularly at all of the bridges and tunnels, which any road vehicle is going to have to take.

In contrast, if you take the E train from Sutphin Blvd, where it connects with the JFK AirTrain and the LIRR, you could be in Manhattan within 30 minutes (a total of eight stops as the E runs express in Queens during the day) and at 56th and Third within 45 minutes, and I think I'm being very conservative with my estimates. If you take any road-bound transport into the city from EWR -- and I'm including taxis and car services in this as well -- you could easily spend that much time just at the Lincoln Tunnel entrance, let alone the traffic you're going to have to negotiate once you get into the city.