Nexusmods is legit.

As for those files, a mod manager is just that, a mod manager. Just a program which makes it easier to install and uninstall mods. NVSE is a plugin which allows modders to use additional commands and perform additional actions which go beyond what can normally be done in NV. JIP is an addon to NVSE which enables even more stuff. And (as I'm guessing you know if you're planning on installing it), the JSawyer mod is a mod which attempts to rebalance aspects of the game to make it closer to the stated vision of Josh Sawyer, who was the lead designer on NV.