Both have their respective advantages and disadvantages.
Toad Sage Mode is weaker in raw power compared to Gates (I'm referring to taijutsu department), but thankfully it does not have the deadly side effects of using Gates (even though I'm not including 8th Gate).
Entering Gates is relatively quicker than SM, which is not easy to enter in middle of battle because collecting natural energy takes time. But this disadvantage can be nullified later on with further practice which will lead to quick entry in SM.
Both have their own time limits. Gates can actually stretch out longer but it takes a heavy toll on your body. The time limit of TSM is quite less if you haven't prepared additional clones to collect natural energy. Even then reverse summoning those clones in midst of battle would be difficult. But taking the hassle of clones and reverse summoning won't be required if SM can be quickly entered.
But the biggest advantage of TSM over Gates is in the ninjutsu and genjutsu department. It's not limited to strengthening just taijutsu like Gates. And depending upon what kind of ninjutsu and genjutsu you have, SM can range from being just strong (like Naruto) to godly strong (like Hashirama).
Overall, I think TSM is a better choice because the disadvantages of TSM (like slow entering and low time limit) can be remedied and made non-existent with further practice while the disadvantages of Gates (like heavy body pain) keep pertaining. But the main reason is that although TSM will be weaker in taijutsu, it will have strength in ninjutsu and genjutsu which Gates have zero advantage in. And having a powerful ninjutsu to accompany with TSM can make it really strong, much stronger than Gates unless you plan to die.