The full pipe sections could be rolled into 2 to 3 foot of water. I'd put a rope through them first (not tied, just through the pipe) to use as a method of control so they don't roll deeper than you want. All the while have a buddy holding onto the two ends of the rope. Then, approach it with the pontoon and see how easy it is to lift off the bottom. 100 to 150 pound should not be to bad to lift up a few inches and tie it off to the boat....back the boat out to where you want to place it, lower it down, then let loose of one end of the rope and pull up on the other.
Horizontal versus vertical placement might be difficult, but I'd go for the hole being horizontal (pipe laying on it's side) and if a few ended up vertical...so be it.
Consider leaving the rope on the first one placed with a milk jug tied to it so you know where it is for bunching more around it if bunching is your plan. Remove the jug once done...or tie a cheap duck decoy to it so you know where there are.
I would hesitate doing this with my 12 foot boat (hesitate...lol), but a mini-pontoon and a buddy for driving the boat and ballast weight would work well I'd think (given the pipes don't weigh too much).
