How big is too big? 4-5" isn't too long to snap off the side shoots - push them to one side so they snap cleanly leaving less of a wound. If they are a foot long then that may well be too long and you would be risking infection to remove them.
If there is just one really long one per plant then I would leave it, and just have a bifurcated plant. Give each stem it's own stick, with plenty of space between them for good air circulation. If there are more long ones than that, then use a very sharp knife, sterilised between each cut (with meths or white spirit) to cut them close to the main stem, but taking care not to damage the stem.
For future years, give each plant a cane when you first plant them out, and tie in the main stem as it grows, and take out the side shoots when they are just an inch or so long, by snapping them sideways (pricking out is where you take seedlings out of a seed tray and prick them out into more spacious quarters). So you need to be doing something with your tomatoes at least every 2-3 days. I find tying in my toms very relaxing. I don't side shoot as I don't grow indeterminate varieties.