Which is it?

IMO (i.e., no reference link, no style-manual authority, but this is how I'd do it):

"Was this it?", John wondered.
-or-
Was this it?, John wondered.

If you're writing in a tight POV and this is internal dialogue, you don't even need the tag.

Was this it? and then go into whatever action John has next.

Was this it? John looked up at the monument thoughtfully.

Or whatever. That's what I'd do--lose the tag entirely.

Dang, that's a good suggestion.

<---occasionally helpful, but usually only by accident.

I like mscelina's suggestion.

If you were going to add the dialogue attribution, you could use a third option: Was this it, John wondered.

Or, if you use a question mark with quotes, don't use the comma: "Was this it?" John wondered. But technically this is wrong, as mscelina said, because it is not really a quote, but a thought, and is usually italicized with the attribution dropped.

Never commas after question marks in quotes of any kind.

So post 2 is out? What would be your recommended approach? This is a situation over which I puzzle.

I puzzle over these things too. But in this case it's a reported thought. In real time, it would be: Is this it?

Seriously, I'd take the gutless approach and reword the thing. Make it clear in context that we're in John's head and then just throw the thought out in italics.

Failing that, I'd dig up a really good style guide and see what it had to say...