I have RPi3 connected to the TV via HDMI. I'd like to have another connection (via VNC for example) and start presentation which will be displayed on that TV connected via HDMI. Is it possible?
This is doable, but it isn't necessarily a raspberry pi issue, it is regarding the Graphical Desktop Environment on your RPi3 and using it to display content from another source/stream.
There are a large number of possible solutions, depending on many details. VNC is certainly doable and probably the quickest and easiest in the short term, if the VNC server will run on the Raspberry Pi 3.