New York City - Question regarding cab fare

I know from JFK to manhattan (staying around time square) is a flat fee, just wondering if that applies during rush hr as well?

Yes, but there is a $1 surcharge between 4pm and 8pm. Although I'm actually not sure if that applies to the JFK flat fee. It will probably tell you on the TLC website.

I don't think the $1 afternoon surcharge (or the $.50 night surcharge) apply to the $45 flat JFK fare.

But the $0.50 state surcharge definitely does. And there can be tolls depending on the route you take.

http://www.nyc.gov/html/tlc/html/passenger/taxicab_rate.shtml