What about Roserade, Virizon and Shaymin? The Rotoms? Especially the lawnmower variant. Even Celebi can do work. Not to mention things like Toxicroak and Cacturne can cause problems for some of Manaphy's sets.
In the end we have other bulky waters with setup in the tier in Suicune and Slowbro. The main things which differentiate Manaphy from the others is a higher speed tier, better coverage options and Tail Glow. I think Manaphy may actually be rather close for me, as we have quite a lot of things in the tier that do very similar things to it already, other than Tail Glow.
The problem is none of those pokes except for Virizion can actually swap into manaphy and guarantee forcing it out while it boosts with tail glow. I really don't consider speed ties to be acceptable since that would be a very unskilled way of dealing with manaphy (to state the obvious, the 50/50 in who moves first is in no way reliable). As for toxicroak and cacturne.
252+ Atk Life Orb Cacturne Sucker Punch vs. 0 HP / 0 Def Manaphy: 172-203 (50.4 - 59.5%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
252 SpA Manaphy Ice Beam vs. 0 HP / 4 SpD Cacturne: 246-290 (87.5 - 103.2%) -- guaranteed OHKO after Stealth Rock
No good for cacturne, and even worse if manaphy is +3
+3 252 SpA Manaphy Ice Beam vs. 252 HP / 4 SpD Toxicroak: 289-340 (78.1 - 91.8%) -- guaranteed 2HKO after Stealth Rock
252+ Atk Life Orb Toxicroak Gunk Shot vs. 0 HP / 0 Def Manaphy: 243-289 (71.2 - 84.7%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
Toxicroak falls agonizingly short, except with very favourable damage rolls where it can trade itself for manaphy through gunk shot and sucker punch but dying from SR + LO recoil and +3 ice beam. Unfortunately this is also with a subpar EV spread for toxicroak too.
Next best option in that list of grass types would be Rotom-C if it had a choice scarf attached to it, but that's as good as it gets.
Edit: I also remember Kokoloko talking about how its a deadweight vs offense. While that might be true if you just blindly attack manaphy, here's a few more interesting calcs in which manaphy can survive an offensive poke trying to take it down before it gets to use tail glow boosted attacks against you. Note that all of these pokes are faster than manaphy either naturally, or through use of choice scarf and that the assumption is that you swap one of these pokes in as manaphy uses tail glow.
252 Atk Life Orb Mienshao High Jump Kick vs. 0 HP / 0 Def Manaphy: 269-317 (78.8 - 92.9%) -- 37.5% chance to OHKO after Stealth Rock
252 Atk Victini Bolt Strike vs. 0 HP / 0 Def Manaphy: 238-280 (69.7 - 82.1%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
252 SpA Hydreigon Draco Meteor vs. 0 HP / 4 SpD Manaphy: 205-243 (60.1 - 71.2%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
252 Atk Azelf Explosion vs. 0 HP / 0 Def Manaphy: 265-312 (77.7 - 91.4%) -- 31.3% chance to OHKO after Stealth Rock
252 SpA Sheer Force Nidoking Thunderbolt vs. 0 HP / 4 SpD Manaphy: 192-226 (56.3 - 66.2%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
252 Atk Choice Band Iron Fist Infernape Thunder Punch vs. 0 HP / 0 Def Manaphy: 252-298 (73.9 - 87.3%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
For a pokemon running no bulk, that's pretty damn good that it can survive those STAB or SE attacks. You really do need a faster grass or electric type to ensure you can strongly check it, as the STAB is really important.