If it were me, there'd be no contest, it'd be the Sunn all the way. $1000 is usually the price of a head alone, and that rig will end up more valuable than the SVT-CL to a good many people. Besides that aspect, I also just think the Sunns sound better than the SVT-CL (and SVT-VR) by a country mile. I've never played a vintage blueline or anything, but I've tested out plenty of newer SVTs, and I don't think I'd voluntarily play through one given the option to play through a Sunn (or Hiwatt, or Marshall, or Sound City, etc). However, this is all personal opinion, there is no objective fact that one is superior to the other. For my tonal goals, Sunns do it, Ampegs don't. Here's a sample of my 1200s, controls set vol. 5, treble 10, bass 2, contour 10, to give you an idea of what tone they can produce. That's just a precision with rotosound swing 66s.
As far as durability, the Sunns are built like tanks. The transformers are like having two grape fruits stuffed in the head cabinet.The insides are very nicely laid out PTP, and can be easily serviced by most competent techs, as the design is in part derived from old Dynaco Hi-Fi stereo circuits. Which leads to another point that should be considered when comparing these amps: the 2000s is rated at 120w, but people will say "it's a very loud tube 120w". What they are actually perceiving is that if we were to measure the 2000s by the same standard as the SVT or most MI amps, then a healthy one would more accurately be rated around 190w. Sunn rated their amps by Hi-Fi standards, quite a bit more rigid than MI standards, and thus the 2000s was 120 watts RMS continuous, 20 Hz to 15 KHz, within 1 dB of 120 watts with less than 1% total harmonic distortion. So it's 120w in the 20Hz to 15KHz frequency range, before any THD (or, well, 1% distortion), so you're getting 120w clean before any trace of breakup. Pipe that into JBLs, very effecient speakers, and you have a very loud rig despite it's relatively "low wattage". Trust me, I run both a 1200s and a 2000s into 2x2000s cabinets each loaded with JBL K140s. That's a loud freaking rig. It does feel as if the air is blowing from behind you. The SVT will still be louder, but it's not as big of a difference as it might be made out to be.
What would be important to discover is what speakers are in the cabinet. As Satori said above, the 2000s only ever came with JBLs (although artists could pretty much ask for whatever speakers they want, so there are supposedly some factory Altec loaded 2000s cabs), but who knows what condition they're in, or even if they're the original speakers.