Jim-D, you didn't mention for which purpose you're buying these rifles. Collection or utility?
If it's the latter, then my personal preference would be the Marlin. The ammo is available everywhere, the Marlins are very easy to maintain, and I have always liked the way they felt.
If the former, then I suggest buying the one with the best investment potential. The Savage 99 has its own distinct following. The older Marlins have a fan base too.
You can't go wrong with either performance-wise IMHO, but in a strictly utilitarian sense I feel the Marlin would serve a bit better and be easier to move should you ever decide to sell later on. The more common chambering in a well recognized aesthetic profile increases the number of potential buyers more than two-fold.
As suggested previously, buying both would end the dilemma and add two great rifles to your stable. No regrets in the hind sight department either.
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