I reminded him that we went Indy before the NY6/playoff structure so I'd double check that

BYU did go Indy before the current playoff structure and NY6.  This started in 2015.  The better date to consider though is 2012, when the highest ranked G5 champ was guaranteed access to a BCS bowl game.

Still accurate to say the choice to go Indy was prior to that though, so you're correct there

under the current structure, do we have easier access to NY6 bowls than BSU (or any other G5)?

Probably not.  G5s have two options to get to the NY6 - either at-large or by getting the automatic bid for the highest G5 champ.  BYU can only get there through an at-large bid.  Given the numerous conference affiliations and difficulty in being Top 11 in the country, I'd say that G5 teams have it easier.  As evidence you can consider the number of G5 teams who have made it while BYU has not.  You're also seeing it this year - even against a stronger schedule, we basically have to go undefeated, whereas Boise or Memphis or the like can go undefeated (or sometimes even lose a game) against a weaker schedule and get the auto-bid.

He said the MWC champ is an automatic to the NY6, but I said it's the highest ranked G5 champ who gets an NY6 

You're right, he's wrong

do MWC teams, particularly BSU, get to keep more money if they get bowls?

There was a tug-of-war between the AAC and MWC for Boise and so Boise was able to get a number of special concessions from the MWC.  Their games were sold separately from the rest of the conference for TV purposes, and the rules were changed to enable schools to keep more (if not all) of their bowl money.  Gonzaga was able to use their influence to do something similar in the WCC, retaining pretty much all of their NCAA tourney $ (only sharing the first unit that the conference would have had anyway without Gonzaga).

Considering BYU's impact, it's likely they could have requested and received similar (or possibly better) concessions as Boise St did.