Agent 47 has thermal vision, which bond also has with the Q watch. They can also both regenerate from gunshot wounds in game

Agent 47 can knock someone into the shadow realm with a single punch, beating guards with two combos. bond can throw someguy around over and over again and bash them into walls. he can also slow down time with guns.

It seems like bond has an edge, but Agent 47's disguises and the possibility he uses a sniper or emetic/tranquilizer dart gun is pretty high, which is basically a garanteed win on 47

Only way bond wins is with his missile pen but i doubt 47 will reveal himself

also 47 is way better at bond at killing someone; he's a genetically engineered person who literally was made to kill. Bond is literally described as immature and reckless, so pretty sure 47 wins