You can use In-System Sources and Probes (ISSP). It allows you to monitor various signals in the design on the device with a JTAG interface. May refer to below link for details related to Design Debugging Using In-System Sources and Probes
Note that In-system Sources & Probes is only "real-time" as far as how fast signal info is sent over the JTAG connection, so you're talking about kHz speeds. You're not going to be able to see high-speed signals toggling with ISSP.
Signal Tap really is the main debug tool for looking at signals, through they are frozen at a moment in time.