Yeah, it's a good question! I agree a case can be made for all of them (Ted Green actually thought the '86 team that lost to Calgary was the best of them all). The '87 playoff team -- adding Nilsson and Ruotsalainen -- was probably the best team on paper, but I'm not sure about in reality.
So, my choices are as follows:
1) 1985 - Don't be fooled by the more modest 109-point season and 2nd-overall (to Philly) finish. Before a late-February/March slump (which was more due to indifference than anything else) the team was 43-12-6, and that was with Messier missing 35 games. As soon as the playoffs started, they woke up and went 9-0 to start the postseason, outscoring teams exactly two-to-one. Coffey and Gretzky and Kurri were never better than in this season, including the playoffs where Gretzky was at his pinnacle. Tikkanen even joined in time for a few games in the Finals!
2) 1984 - I don't remember this one as well because I was pretty little, but they trumped the League with a 119-point season, finishing 15 points ahead of their rival, the second-overall Islanders. This, despite going 1-5 in the six games Gretzky missed. Gretzky was completely otherworldly in November '83 to January '84, scoring at the highest pace of any player, ever. Messier's move to center in late season consolidated the second line. Highest-scoring team since the WWI era, and had Anderson got one more point, they'd have had five 100-point scorers.
3 ) 1988 - The team was not the favorite to win this season, and was surpassed in the standings by Calgary. So, I think just by virtue of a good-but-not-overwhelming regular season, this team can't be ranked higher. Also, there is no Coffey, no Moog, no Nilsson, no Ruotsalainen. And yet they went 16-2 in the playoffs, the best record in the four-round era. Given all the off-ice drama over the team (losing Coffey, Moog), Gretzky's missing 16-games, playing the same goaltender in every game, and general team indifference to the regular season, it's actually impressive they did as well as they did, in retrospect. This team could play serious defence for the first time, minus the rover (Coffey), and with Fuhr and Ranford, were incredibly set in net. They had to beat three really good teams and one decent one for the Cup, too, so the 16-2 is all the more amazing (including a 4-0 sweep of the 1st overall Flames).
4) 1987 - As I said, this is the best team on paper. Maybe the most talented offensive line-up ever in the NHL, come playoff time. But performance-wise, they didn't impress quite as much, I think. They dropped game one of the playoffs to L.A., and had to struggle to win games three and four. They lost badly in game one against Detroit, and had to struggle to get through the rest (Gretzky may have been concussed, but put up a measly two assists in the series for his worst playoff production, ever). Then they blew a 3-1 lead against Philly and nearly lost the Cup. Gretzky later said this was the first season in which he was physically drained late in the regular season.
5) 1990 - This one is close to my heart and might be the easiest team to love, but minus Gretzky and Coffey, and following a modest 90-point season, they can't be the best team. But they were really solid and generally under-rated going into the playoffs. They swept aside the Gretzky-Kings and easily took down 1st-overall Boston, despite Ray Bourque at his peak. (This team, of course, also later traded for Brian Leetch and won the '94 Stanley Cup as well. Whoops! Did I say that?)