I'll try to answer my best to this question but befor i need to underline 3 major points :

1. ''what did they think'' is a pretty large question so i'll try to cover the basics but don't hesitate to ask for more details .
2. the Native tribes in Québec aren't a single bloc and didn't all react the same ways to the separatist movement and the PQ (for example the mohawk tribes which speak more english and is historically closer to english canada didn't react the same way as Abénaquis who speak more french) .
3. by ''the separation crisis'' i'll assume you're talking about both referendums and not the octobre crisis, and as a period as long as that (1976 to 1995) the government changed, the relation which each aboriginal group changed a lot in almost 20 years, i'll only cover the 1995 referendum, if you want more details about it i'll gladly go in more depth.

That being out of the way, the Québec independance movement wasn't really well recieved by natives in general. To give you an idea : the yes received a support of 9,6% of votes in reserves and nordic villages. Those stats go up for french speaking natives : 11,5% for Montagnais, 22% for Hurons and 25,5% for Abénaquis. Also inuits voted 14,6% for the Yes. We can clearly see that the winning position was No amongst natives.

Now a question arises : why ? After all the PQ promised nation to nation relations between quebec government and his native populations, the creation of new laws which would be written with all native communities and reserves to replace the ''canadian colonial indian law'', more financial autonomy that would lead to less dependance on financial help in the long term, the option to create native governments with full recognition from Québec's government, a new teamwork approach to regional developpement which would encompass sustainable developpement and native rights, etc.

A part of the answer lies in the official response that the grand council of the Crees wrote in the form of ''Sovereign injustice : forcible inclusion of the James Bay Crees and Cree territory into a sovereign Quebec'', a 500 page study (which approaches the question mostly from a moral and legal perspective) which concludes that a winning referendum for Quebec's independance ''couldn't forcibly include'' aboriginal people and their land. Essentially, the attempt to include aboriginal people in a new quebec isn't generally seen as an offer for a new possiblity for a equal future from nation to nation but as a new colonial force which would try to controle their lands (if this vision is accurate is entirely another question and is still cause for debate). It is also important to note that historically the crees are closer to english canada (for a lot of reasons, one being that for more than a century their only contact to the european world was the Hudson Bay Compagny) and that relations between Quebec and the cree are going better since the ''Paix des Braves'' in 2002.

The Oka Crisis of 1990 (which opposed mohawk people and the town of Oka) is here a good example of the tensions between Mohawk and quebec (so its easy to see why they weren't really simpathetic with the separatist movement in Qc).

TLDR : the Quebec separatist movement and the PQ offered the first nations the opportunity to change or abolish the colonial relation they had with canada with a lot of reforms but it was perceived as a colonial gesture to not let aboriginal communities choose on their own if the'll join quebec or canada.

Sources:

Vanasse, A. (1998). Donald Smith : D’une nation à l’autre. Lettres québécoises, (89), 7–8. ( https://id.erudit.org/iderudit/38110ac)

Drouilly, P. (1996). Remarques sur le référendum de 1995. Bulletin d'histoire politique, 4 (3), 5–10. https://doi.org/10.7202/1063541ar

Goulet, J.-G. A. (2006). Maîtres chez nous : les fondements des projets de justice et de citoyenneté des autochtones et des allochtones au Québec. Anthropologie et Sociétés, 30 (1), 187–201. https://doi.org/10.7202/013837ar

Trudel, P. (2017). La souveraineté du Québec et les peuples autochtones. Nouveaux Cahiers du socialisme, (18), 54–59. ( https://id.erudit.org/iderudit/86366acadresse copiéeu )

Grand Council of the Crees. (1995). Sovereign injustice: forcible inclusion of the James Bay Crees and Cree Territory into a sovereign Québec. Nemaska, Québec.