Lifting the trailer a few inches to change a tire won't shift the CG enough to topple the boat. At a marina that I worked at, we had a trailer similar to yours that we used to move boats around the yard. We (I) routinely jacked up boats to position the trailer beneath it. An axle broke once and you'd be amazed how far a trailer can tilt without the boat falling.
A picture of the trailer from the rear would be helpful, but I'd position the jack beneath the axle as close to the tire as possible. As I lifted the boat, I'd place wood blocks (vs. cinder blocks) beneath each corner at the rear of the trailer to stabilize it.