Advise please!

Frames - toss of the coin. Both are aluminum.

Forks - Toss of the coin, both are low budget.

The hierarchy of Shimano parts... +1 Fantom
XTR > Deore XT >Delore SLX > Deore > Alivio > Acera > Altus>Tourney

Brakes: Hydraulic brakes generally stop better than mechanical but mechanical are much easier to work on and adjust (read: bleeding hydraulic brakes is a PITA and bout $80 if one takes the bike to a shop). +1 for Fantom

Wheels/Rims/Tires - +1 Fantom as they are 36 hole. More spokes SHOULD be more durable. Both have WBT tires - the Phantom's are very slightly narrower (2.2" vs 2.1"😉

No idea if Nashbar or Bikes Direct will do a better job prepping the bike.

I would not buy either of those two bikes because they both have suspension forks and cheap suspension forks can be a real nightmare. You would be better off trying to find a bike that has solid forks, and because the solid fork is less money than a suspension fork you'll end up with better components to make up the cost savings.

If for some reason you want a suspension type of ride consider instead getting a aftermarket suspension seatpost, these are a lot cheaper than a fork and will last longer.

The bikes are all good. With the same price means they have the same quality. All you need to do is compare reviews in their sites to see any extra unique feature. What is their guarantee period? If different then choose a long term guaranteed bike. But I will go with the Phantom.