It's an interesting question. The real difference seems to be burner & heat exchanger design since the OEM gas valve and fan choices are so limited. The contractor folks I talked to weren't interested in selling anything without a stainless steel heat exchanger. After that the major consideration seemed to be price with the Munchkin winning that battle. There may be some good deals going with a Munchkin and SuperStor together since HTP makes both.
Buderus has an edge on efficiency and may qualify for tax and/or utility credits/rebates. They are expensive though that might not be a major hurdle with the high gas prices you face in Brooklyn.
Make sure your contractor is comfortable and experienced with the brand you're interested in. You don't want to be their "learning curve."
Most folks seem to say stay away from coils for dometic hot water and use the sidearm tank.