No matter how you define 'good' or 'great', the list has to be short since there are only five players who were the starting QB for the Pats for more than three years (Parilli, Plunkett, Grogan, Bledsoe, Brady), one for three years (Eason), and two for two years (Hugh Millen, Butch Songin - and neither of them are going to make this list.)
Flutie can't really be considered in my opinion because his good-greatness happened elsewhere; he only started a total of 13 games at QB with the Pats.
If you are going to compare players from different eras, such as Parilli and Plunkett, keep in mind how the passing game has changed - specifically what the defense can and cannot do. Rather than looking at numbers like passing yards or completion percentage, a better gauge is how they ranked against their contemporaries.
Parilli was good but not great. Here is how he fared against his contemporaries:
1961: 1st in pass completion %; 2nd (best) in interception %, passer rating, td %
1962: 1st (best) int %; 2nd td %, completion %, passer rating, yds/pass attempt; 3rd in passing td, comp/game (14 - think about that!)
1963: 1st team all-pro and pro-bowl; perhaps in recognition for the previous season; yards/pass (2nd) was the only positive ranking.
1964: A pro bowl and 1st in passing yards, passing td's, passing yards per game - and interceptions.
1965: 2nd in passing yards and passing yards per game.
Those are the positives, but here are the negatives:
'63-67: no better than 5th in completion %, 4th in int %, 4th in yards/attempt, or 4th in passer rating - remember, the AFL had only 8 teams through '65 and 9 in '66-'67. Parilli was Favre-esque in this time, leading the league in int's once and finishing in the top three for most int's for five straight years.
As far as Plunkett goes, he was on some very bad teams, which skew his stats. He was sacked at least 36 times in each of his first three seasons in an era when teams passed less often and the season was two games shorter than it is now. He was beat up so badly with the Pats and 49ers that he needed essentially two years off before he was useful again, having a few very good seasons with the Raiders. Obviously not in the 'great' category, but he was better than his 23-38 won-loss record would indicate; the team's problems at that time were at other positions than QB.