I heard Lee's Performance does a good job at a fair price. You just pull your ECU out and mail it to their shop. Turn around time is like 6 days. I think they charge $100 for the service. That is a good price compared to other places. Just be sure to go to a reputable shop.
If it is a track/race bike, I say go for it. You wont even notice a difference on a street bike.
That said, there are a couple of places that can flash your ECU. Personally, I purchased the cable from Flash-Tune and do my own flashing but they can do it if you mail your ECU to them. Gruhl is another name that comes up, and I am sure there are plenty of others.
I got my ecu flashed by lees I had my rev limiter raised 600 more rpms so it redlines at 16000. Every gear redlines at 16000 except 6th won't go past the stock 15400. So there for I'm not getting any more top mph does anyone with a 2013 zx6r thats flashed do this too?