I grew up being taught to never let the canoe touch any rocks or the shore, which meant always jumping out of the canoe before beaching. I still follow that practice, which means wet feet. I use high top leather boots.
Whether you follow that practice, or if you want to strive for keeping dry... it is important to select footwear that gives you plenty of ankle support. Your boots must be the right size so they do not shift. Portages can be very rugged and rocky and you need to have foot wear that will protect you on those jaunts.
It is often difficult to keep your feet dry... even if that is your goal... Many portages have low lying areas that can be wet, muddy, or even submerged. During low water times, you may need to walk your canoe through some areas on streams, or you may choose to walk your canoe through a channel rather than portaging.
I do not recommend tennis shoes, water socks, rain boots, or flip flops as your main footwear. I do recommend packing a pair of water socks for swimming though.