It probably isn't the level as much as the quality of program within the level which is where you will find your answer.
Since your son is in the NECBL, it serves as a good example/illustration. Newport, Keane a couple of others can compete with just about anyone in Summer Wood bat leagues. They can go over to the Cape and compete. They might not be the top team but most years Newport and Keane are certainly in the discussion with the next level of Cape teams and Northwoods Teams. It moves down a bit more rapidly in the NECBL however and the Cape and Northwoods might have more depth of better teams.
The way I would look at this is as follows:
For NAIA, if you are talking about programs like Lewis Clark State, Oklahoma City and some others, they are close to mid level DI and top level DII. It moves down from those so that more than a few are closer to mid-level D3.
At the D2 level, schools like Tampa, Delta State, SSU, UCSD and many others are certainly competitive with mid level DI.
JC's are tougher to quantify because CA. follows a very different classification than TX and does not provide scholarships, etc. Generally, through, top level JC's in TX, FLA, CA, AZ, etc are going to be darn good but not DI or probably the upper levels of D2.