i just get some cheap black planters (usually the ones plants come in when you buy them at the store) fill them up with regular soil, and add a thin layer of gravel on top. works for me!
For the ultimate in cleaning out a pond, my pond store rents for the day the Oase Pond Vac: http://www.islandnet.com/~pondusa/pondovac.htm
I used it before the summer and there is absolutely nothing it can't suck up.
If you are rich - and have a shed to store it - this is the way to go.