They're both renowned bounty hunters in their respective universes, so I wouldn't put either's reputation or skill set above the other's. What breaks the tie for me is that Samus has way more toys. She has a plasma gun, a stronger plasma gun, a fire gun, an ice gun, a gun that shoots missiles, bombs, and a variety of armor. She regularly kills Space Pirates, and Boba Fett isn't far off from that. She also kills powerful aliens who are planetary threats by herself, as well as swarms of lifeforce-sucking parasites and CYBORG PTERODACTYLS. I see no reason why Boba would give her problems when aberrations like Mother Brain, Metroid Prime, and the CYBORG PTERODACTYLS don't.