The last achievement for the Minutemen is "Old Guns", which is odd because unlike the other factions, the story continues on for some time after that (provided you make certain choices).
The last achievement for the Railroad is "Rockets' Red Glare", but if you get it, you can't get the achievement for "Underground Undercover", so make sure you finish that mission first.
The last achievement for the Brotherhood of Steel is "Ad Victoriam", but because you're forced to make a choice in "Mass Fusion", the ending to the Brotherhood or Institute storyline will be closed off. However, you can get the "Blind Betrayal" and "Liberty Reprimed" achievements before you start "Mass Fusion".
The Minutemen, Railroad and Brotherhood will all give you "Nuclear Option", since it's effectively the same mission for each faction, even if the particulars differ.
You can only get the Institute achievements if you take their side in "Mass Fusion". "Mankind Redefined" and "Powering Up" are easy enough; you can pick them up without destroying your relationship with other factions. In the same way, "Nuclear Family" is only possible if you side with the Institute at the end.