The main element when building a sub enclosure is for it to be rigid. MDF naturally has more "flex" than a good plywood so generally it would need to be braced better. But most here would say that EVERY sub should be braced well so it's really a moot point. For those of us on a budget MDF is significantly cheaper though.
Since you're using a Sonotube, I think MDF would be the way to go since it is heavier. This will give you more weight at the bottom to reduce the odds of it tipping over. For a sonosub just make sure the end caps are nice and tight and you should be good to go.
By the way, I'm just over the boarder in Ft. Mill/Rock Hill if you want a hand.
Feel free to send me an email. 
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