I'm actually re-watching Gintama right now (coz it's awesome) on Crunchyroll and it's as safe as it has ever been.
But if you're certain Crunchyroll just ISN'T working out with you, well then back when I first watched Gintama and most of the episodes weren't released/were for members only I went to these sites. All of these players are generally well working players (Myspace player, Veoh player and so on)
http://www.anilinkz.com/search/anilinkz/Gintama/
No adds

but I prefer the above one more
http://animefushigi.com/full-anime-list/on-going-anime/374-gintama
http://onepieceofbleach.com/?s=Gintama&submit.x=0&submit.y=0
All great, safe, and reliable places to watch Gintama at
http://animeseason.com is also an all around great site to watch anime online, but only has the first 125 episodes of Gintama, and is REALLY slowly putting up more. Gintama has 186 episodes so far, and of the sites I told you OnePieceOfBleach and Anilinkz have them all, since AnimeFushigi only has up to 184 as of right now.
Gintama is such a FANTASTIC anime but it gets little attention from anime fans outside of Japan D: