Although similar questions have been asked before on this FAQ, they didn't address what I was experienceing. So I asked this question in the IRC page and got it working with the help of friendly folks there, so I'll answer myself.
First of all, make sure you have i3 version >= 4.5. The version included in the Debian Wheezy repos is 4.2, which will exit with an error "XKB not supported by X-server".
To install on Debian Wheezy, I had to enable the backports repository by adding:
[web search for how to add backports, I don't have enough 'karma' to post the deb line cause it has a http link in it]
to /etc/apt/sources.list (replace 'ftp.us.debian.org' with your favorite mirror)
and installing i3 version 4.5 like so:
aptitude update
aptitude -t wheezy-backports install i3
Second, make sure the ~/.vnc/xstartup file has the Xsession line commented out or removed, and "i3" or "i3 &" (without quotes) is the last line.
#!/bin/sh
xrdb $HOME/.Xresources
xsetroot -solid grey
#x-terminal-emulator -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" &
#x-window-manager &
#Fix to make GNOME work
export XKL_XMODMAP_DISABLE=1
#/etc/X11/Xsession
i3 &
You may also have to use the line "DISPLAY=:1 i3" instead, if you plan on running the VNC server in a different display (replace '1' with your chosen display number).
Third, make sure you have a terminal emulator installed. I did not, and after getting i3 working over VNC, I could not open a terminal by pressing $mod+Enter. I installed rxvt, but you may have another already installed, or choose a favorite.
Fourth, running i3 in a VNC session will create a bad config file with all the key bindings replaced with "Mod1+(null)". I just copied a local config file over but you can also copy the one from /etc/i3/config.