Okay, some information.

When Tom was in NYC in June, he stayed at the Crosby Street Hotel. He was seen exiting and returning to the hotel carrying his laptop and a manila envelope on June 17. In the second photo you can see the contents of the envelope - a large stack of papers.
http://ww2.sinaimg.cn/large/6e14d388gw1f4ywyxrm3vj21fi2591ky.jpg
http://ww2.sinaimg.cn/large/6e14d388gw1f4ywz93ti8j22002zl4qp.jpg

Balthazar, where Tom was spotted having lunch today, is literally around the corner from the Crosby Street Hotel. Based on this, I'd say it's likely he's staying there again.

According to the following article, Tom's legal team is the Peikoff Mahan Law Office.
http://deadline.com/2014/06/tom-hiddleston-to-play-country-icon-hank-williams-and-will-sing-as-well-787811/

Peikoff Mahan's office is only one mile from the Crosby Street Hotel.

My conclusion: Tom stays at the Crosby Street Hotel when he's in NYC to meet with his legal team.