Robbiedawg has identified the Shin-Etsu wonder grease that Honda sells for the gaskets on the NSX. However, this is not a sealant. It is the equivalent of the deep cleansing facial moisturizing rejuvenator for the NSX Targa and door gaskets (also available at the L'oreal cosmetics counter :smile
. It is not a sealant. You massage it into the gaskets to keep them in good shape.
I am guessing that the seals you are referring to are the two rubber gaskets mounted directly on to the Targa roof panel, one above each side window? The installation process for these seals is complicated (6 pages long in the service manual). The manual refers to the use of 0.5mm butyl tape, 3.0 mm EPT sealer (which is not a sealant) and sealant part # 08712-0004. The manual does not provide part numbers for the butyl tape or the EPT sealer, so I don't know whether that means this stuff is supplied with the replacement targa seal or whether you have to source it separately. There are a bunch of different locations where you have to use the sealant, tape or EPT or combinations of the three. You really need to down load the section of the service manual dealing with the targa top form the NSX Wiki.
The three items, butyl tape, EPT and sealant are required to correctly attach and seal the gasket. If your gasket is not flopping around, I expect that it has already been attached with the sealant and butyl tape.
Check to see where the water is coming in. Is the water coming in between the glass and gasket surface? If it is, then the Shin-Etsu grease may help a little bit since the grease is hydro phobic. But, if you put enough grease on the gasket to seal out water it is going to leave a greasy smear on the glass. The problem may also go away as the gasket conforms to the top of the glass and provides a better seal. If the water leak is bad, you may need to adjust the in/out positioning of the side glass to get a better seal. Door glass adjusting is not trivial so do it as a last resort. If water is entering between the gasket and the roof panel itself, then you may have an improperly sealed / mounted roof gasket.