Short answer is yes. The whole reason /boot is separable is to handle situations where the primary disk can't be read or booted from initially.
The suggested answer in comments is very detailed and long and should be helpful, but let me give a more relevant and generalized answer.
There are multiple options here. If you install legacy, you can actually put only grub on the 16G USB and you can probably merge / and /boot on the 128G USB, and then remove the 16G USB as soon as it is booted to free up the slot. (But put it back when you are running updates in case grub gets updated!)
If you install EFI, you can put the ESP on the 16G usb, but make sure you unmount it before you pull it out. (eject /dev/sda (or whatever the device name is) should unmount both partitions if you put them on the 16G.)
In either case you can probably put /boot on either usb, unless grub has trouble finding it on the 128G usb. If you do put boot on the 128G usb, you should not specify it as a partition and just let it be in /, otherwise may as well put it on the 16G usb.
The answer linked in comments steps through all the possibilities of putting various pieces in various places with or without windows involved.