While it really depends on the hardware that the fedimint is running on, all else being equal I would consider the throughput of a fedimint to be higher than Liquid. There are no blocks in the fedimint context, transactions can confirm ~ instantly, and they can be confirmed as fast as the mint's hardware is able to swap notes with transaction recipients, which I imagine can be very fast. So fedimints are faster to sync your wallet balance (because no blocks to download) and they can do transactions at the speed of bare metal computing (extremely fast) overall should result in a theoretically higher throughput than Liquid.

Liquid uses the strong federations model, claiming to use tamper-proof HSMs to protect the private keys that secure the federated multisig bridge. It is unlikely that your average mint operator will implement such high security measures, if only due to the high technical and cost barrier to doing so. So that is something to consider. I also agree with k00b that auditability is an important consideration.