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What is the best shipping option? In he past I have shipped with fedex, but their prices have gone up.

Depends on where you are. How much weight you have. And how many boxes You have.
If you’re within region (or one or two off) opening a free account with USPS and ordering free region rate priority mail boxes is probably your best shot if you can’t deliver in person.

After that the national choices are Fedex and UPS.
9 times out of 10 FedEx will be the lower cost choice. And the more smaller lighter boxes you use the lower the rate. 100 1lb 6” cubes costs less than than 1 100lb box. Generally 200 1lb 3” cubes costs less than 100 1lb 6” cubes.

there’s also many localised options from commercial TNT and cannonball to private carriers via uShip. Peripheral

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I would be shipping 1 or 2 12 inch boxes at a time. I'm located in Connecticut which I believe is 1 zone away for regional rate. How do those compare to flat rate?