Yes, I have a pentium 3 with 2 USB ports.
The USB's are not plug and play, I have to install drivers for them?
Windows 98 doesn't have a generic USB mass storage driver, but you can add one yourself (nusb-something-or-other - I may have a copy of it somewhere if someone else doesn't) which works fairly well IME. Some older USB flash drives will have their own drivers for Windows 98 as well (I know some Lexar and PNY drives, for example, do); not sure it'd be worth tracking one of those down, but if you have some old (we're talking like <1GB) flash drives laying around, it may be worth checking if they have specific Win98 drivers.
Removing the hard drive will not be possible since my main pc is an iMac with windows 8.1.
You could always use an external enclosure - pull the drive, put it in the enclosure, plug that into the iMac via USB or FireWire (or whatever it uses) and go about things that way.
How exactly does networking work? It sounds like a nice option.
Honestly it's my preference, when possible. You'd need NICs in all machines, and a router/switch/hub/whatever (if you have crossover cable you can plug them straight into each other). I'm not sure how universal NICs are for P3s - I know mine doesn't have one built-in, so it has to use a PCI card. Most (all?) modern computers have a built-in NIC though. Performance may be worse than pulling the hard-drive depending on what kind of hardware you have and how big the files you need to move are.
What I've done with networking is to just enable a folder or partition as a "share" on a machine, and then move files onto and off of it as needed. My router also supports USB storage, so I leave a large-ish USB flash drive plugged in to make sure I always have some network storage available (e.g. if only one of my computers is powered on).
Candle_86's FTP idea is also pretty slick. 😀