Cut it with a reciprocating saw if you intend to weld the cut piece into something else. Cutting with either a torch or a plasma cutter is going to give you a cut edge that probably won't weld well.

How do you intend to seal the water jacket of the motor once you cut and weld it back together? If its the bottom of a cylinder your trying to repair, wouldn't a sleeve work much better, or is that big of a chunk broke out? Gene