Welcome to the forum.
Yes, the 99 4runner does have a locking center diff...a mechanically locking diff.
Your '03 Disco will be slightly faster due to the new engine in the Disco (from older Range Rover). Your Disco maybe a bit quieter on the highway (wind noise and road noise)...but it does have more drivetrain noise than 4runner. Lastly, your Disco will be more comfortable than 3rd gen 4runner (1996-2002). If you have the optional sound system (harman/kardon), then you would have a better sound system than 4runner. If you have the stock system, then i prefer the 4runner's system.
I drove an '03 Disco for about a month. I found getting into and out of the Disco to be difficult...even more so than my 4runner. I never could get a comfortable driving position. Steering and braking favors the 4runner. Handling will be a tiny bit better than Disco.
For off-roading, the Disco is very good. 4runner is better at:
1. Ground clearance
2. Approach and departure angles (although Disco is better at breakover angle)
3. Lockable center diff
4. Available rear electronic locker
1999 4runners do NOT have ATRAC (4-wheel ABS traction control), like what you have in Disco. Only 2001 and up have ATRAC. But, as above, it does have an optional rear locker from factory...so make sure you get one!
Another point to consider is that the 4runner has rear DRUM brakes, not disc. This is where the Disco has an advantage, especially in mud/water crossings.
As for safety, i "feel" tippy in the Disco. The 4runner has slightly better frontal crash test scores. As above, i feel that the 4runner has better brakes...or more easily modulated brakes. In addition, in the Disco, you sit awefully close to the door...which may be a bad thng in a side collision (but you do sit very high up).
Lastly, and most importantly, 4runner is infinitely more reliable and has a better resale value. The Disco is known to have a very reliable powertrain (noisy, but reliable)...however, the other "minor" pieces are not reliable, such as electronics, rattles, cheap knobs, cheap door lock mechanisms, etc.. The 4runner is just better built from the ground up.
May i ask WHY ARE YOU SELLING YOUR '03 DISCO??
Hope this helps...and good luck in your purchase.