I've gotten good deals from both. If the airfare is dramatically cheaper to TPA it might be worth it. Keep in mind though that you're still 90 minutes from WDW and when on vacation time is money.
Florida airport car rentals charge an airport concession recovery fee. If practical I suggest you look at renting at an off airport location to avoid this extra fee. If I remember correctly the fee at Orlando is about 10% of the rental price. Plus making copious use of the discount codes offered about.
It depends, to a degree, on when the rental occurs. In general I've had better success with lower rates from MCO than TPA but have found very good rates at TPA when I've used Priceline.
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