Can I use mortar to level out a patio made of cinder blocks?
No. Mortar isn't designed to carry span loads, and your block patio will almost certainly sag and settle, meaning your mortar will disintegrate in short order. Proper concrete would even need to be poured at a thickness adequate to span gaps, say 3". 

To my knowledge, polyurethane isn't an appropriate masonry sealer. There are other products for that purpose.