just was curious to see if anybody knows, how would the top NAIA schools fare in comparison to the NCAA
Very few NAIA players get signed or even drafted by MLS teams. Granted, the scouting sometimes is very poor and MLS might miss good players, but generally, MLS tries to get the best college players and they get very few from NAIA whereas they get bunches from NCAA D-I. That doesn't mean NAIA teams can't hang with D-I teams but most of the D-I teams simply have better and deeper rosters.
here are the NAIA players drafted since 2008 (I checked, and no one else has been picked since) http://www.naia.org/ViewArticle.dbml?ATCLID=209853095
In SoCal - several of the NAIA schools have recently (within the last 2 or 3 years) switched to join NCAA Division II...and they seem to be on par with the other Div II schools and conferences in the state. Fresno Pacific Azusa Pacific Point Loma Nazarene Cal Baptist and most recently Concordia (Irvine) all joined the PacWest Conference and have had fairly evenly mixed results against the larger-school CCAA conference (which includes almost all Cal State schools)
CSU San Marcos also joined the group. I think this is their first year eligible for post-season play.
Many of the top NAIA programs play NCAA DI teams in the spring season. Yes, it is just the spring season. But, historically, Lindsey Wilson, Oklahoma Wesleyan, Rio Grande, and some others have fared very well against their DI counterparts.
There are recent former NAIA (10 or so) playing in USL some connected to MLS affiliations. I think if your goal is to go pro you got an equal chance of playing NAIA and being recognized then playing for a poor D1 school. That being said your chance is still very poor. I would almost go the Junior College route and hope a decent D1 School sign you from there. In terms of quality it depends there are NAIA schools with almost no Americans. In 2012 Oklahoma Wesleyan key players were Brazilian and thought they could be competitive with D1 schools and beat Oral Roberts (a bad D1 School) 6-2 - http://www.dakstats.com/WebSync/Pag...sg=MSO&sea=NAIMSO_2012&team=2650&compID=41133 Since some prospects but not as dominating team. This was my NAIA prospect list from last season - http://www.prospectxi.com/2016-naia-undrafted-seniors/ Didic is playing with Sporting KC USL side Swope Park Rangers and is doing well.
That has happened out here on the left coast as well - I know the Point Loma team has played San Diego State and maybe a couple other D1 schools in the spring, and done pretty well against them...
Close to D2 in NCAA. NAIA tends to somewhat reach out to foreign players too because they can be a little older and come in as a Freshman. NAIA tends to be small private schools though.
Yes, very small schools - I recall reading that some of the schools at the national tournament had population around 1,000 students.... I wouldn't be surprised if a NAIA school could beat a D1 school, but the better D1 schools would win most of the time - in season. My opinion - no facts, since they don't generally play the top D1 teams.
NAIA is similar to strong D2 conferences in that they get a lot of talented grown players from overseas that cannot get through the NCAA clearinghouse. Some of them get their grades up/Academic merit and then head up to D1s.