Getbmwparts.com is about the best OEM supplier for a water pump. $422.36 plus shipping but I would also replace the tstat at $91.66 plush shipping. This is about a 3 1/2 hour labor charge and some coolant too so you can see what the numbers might be.
The electric water pumps on this BMW tend to fail at around 50-80K miles so this isn't unexpected. I actually carry a new BMW water pump in my trunk because I am at 55K miles and who knows. It is entirely likely your battery is going south too if this is the original. I would have them replace that since you are paying for labor on this it should be cheaper. Be sure that they register the battery which resets the intelligent battery sensor (it is really a computer with various algorthims) and is supposed to extend battery life which I guess it did if this is a 2006.
If you are a DIY guy you can do this job yourself since the water pump is on the bottom of the car...