say I own 1000 shares of a stock in Webull with $12 cost basis
and also 1000 shares of it in Vanguard with $16 cost basis

stock is currently at $12, if I sell 100 shares from Vanguard do I get to harvest the full $400 loss from that cost basis?
(and alternatively would selling 100 shares from Webull just be break even?)

You can pick whichever shares you want to sell but the basis will remain fixed and reported to you, and the IRS, by each company.. Assuming you sell both for $12 you should have a $400 loss on the entire holdings. If you want the loss but also want to keep the stock, sell the losing position and buy it back 31 days later. If the price hasn't moved you make nothing, lose nothing, but have $400 in the tax loss file.