It's hard to say, because there's a few different subway operators in Tokyo, and if you switch between them your fare doesn't transfer. An example is JR and Tokyo Metro. There also exists Tobu lines, which run on Tokyo Metro lines, but sometimes have a different schedule. In my experience, the base fare (the price of entry) seems a little high, but the price stays the same for the first few stops, meaning that going 2 stops is more expensive than 4 stops. I think this effect continues into longer subway lines, and the prices of going to different stations is staggered if they are close together (e.g. if two stations are close enough, the price will be the same to go to if you come from the same location). I would argue that Tokyo's subway, overall, is probably about the same price if Bart was the same size.
Beyond the price, Tokyo Metro is almost always on time and pretty clean, and generally the delays happen late at night (the delays are only for a minute or two). Having been here for over a month, I've only experienced one daytime delay that lasted more than 30 seconds.