Your getting ripped off. With core charge you can get a reman from Autozone for about $60 and $20 of that is refundable when you turn the old water pump in and if you think that crooked ******* mechanic is giving you one any different than the cheapo one they sell at the local autpart store your very naive. A water pump for a pro mechanic should be done well under 2 hours at the max. A valve cover gasket is about $30 and a pro mechanic can do one in about 20 minutes if he is using hand tools instead of air tools. So thats $90 retail cost, which the shop pays about 25% less than you do on parts because they have a corperate account, so knock that cost down to about $50 in parts for them. Add in some coolant fluid which they mark up about 50% in cost from what you would pay at the parts store even though they pay less. Add in 2 hours of labor at $70-80 an hour even though the mechanic probably only makes $15-18 an hour and then tack on $100+.
Rough estimate
Parts - $50-60
Labor - 2 hours @ $80 per hour = $160
Shop fluids $30
Tax and other BS $20
So ballpark around $270 for a realistic shop estimate
+$160 profit fee because shop knows customer is clueless charge
here is a write up on doing a 4.0 water pump, the vehicle model is different but the concept is pretty much the same on all Jeep stright 4 cyl or 6 cyl motors
http://www.jeepforum.com/forum/f13/jeep-4-0-water-pump-writeup-1117618/