There are pros and cons to each.
The main downside of the LEDs is that no one currently makes a fully contiguous pixel array. If you look closely at any of the LED panels currently available, you'll see that they're divided into little 8x8 arrays that are pasted together. There are visible seams between the blocks. The plasma panels are seamless. (Vishay used to make a seamless amber LED panel that was designed as a drop-in replacement for the plasmas. They might even still make them, and you *can* still get them, but they're ridiculously expensive, around $600.) The other potential downside of the LEDs is that the color doesn't exactly match the classic pinball DMD color; if you want to precisely re-create the experience of playing a mid-90s game, the plasma is a better match. Depending on your point of view, though, that might be an upside, in that you can find LED panels in a variety of different colors - you could go with something unusual and distinctive if you're not aiming specifically for a re-creation.
There are a couple of negatives with plasmas, too. First, they don't last as long as LEDs; the pixels contain gases that leak out over time, which reduces the brightness gradually, and often unevenly - lots of old plasma panels that have been in use for a while have rows, columns, or random pixels that are dead or practically dead. However, the lifetime of a plasma panel appears to be a function of how often it's used - the more it's on, the shorter its life. In arcade use, where machines are usually left on all day, the panels tend to start dying within a few years. If you're planning on home use, where you're only using it occasionally and turning it off when not in use, the lifetime should be very long, maybe effectively infinite. I have a Theatre of Magic that's been in home use its whole life, and its plasma DMD still runs like new. The second negative with plasmas is that they're a bit of a hassle to power on a virtual cab, and somewhat expensive for the extra parts needed - they need several different voltage supplies, some at relatively high voltages. However, VirtuaPin offers a pretty much plug-and-play kit with all of the components you need for that, which largely eliminates the hassle (but there's still the extra cost, of course). I think the LEDs all just need 5V supplies.