Who's call
 

R1 on third base. Fly foul pop up in foul ground just in front of 3B. F5 goes to field the ball and runs into R1 who is about 2 feet off the bag toward home plate and prevents the ball from being caught. Clear interference which was called but after the game partner and I got into a discussion about the umpire,if any, that should have the primary call on this. Two umpire system and NFHS rules not that it matters.

See interference, call interference.

The runner on 3rd is generally the plate umpires responsibility. But with an umpire standing right there, it shouldn't matter who calls it.

Agreed - interference is the call of whoever sees it.

I would expect the PU to make an INT call on a batted ball, except when the INT is in the deep infield on the BU side.
Deep infield being in, near or beyond the 1st-2nd & 2nd-3rd base lines.

PU is already in position to call this: it's the PUs runner, and the PU has responsibility for fair/foul and catch/no catch. So he/she should have all the elements right in view and would have the primary responsibility to make this call.

In the two man system, although BU is over on the 3B side of the diamond he/she has responsibility for the BR running to 1B. Sure it looks like a foul ball but it's not one yet. The ball could fall untouched and backspin in to fair ground. So BU needs to watch BR touch 1B look for possible OBS etc. With more runners on BU has even more responsibility.

Having said that, depending on the timing BU will probably sill get a good look at this and if PU vapor locks or somehow gets screened BU certainly can and should make the call.