Real Identity of Sankara

Sankaracarya was a Vaisnava (not a Saiva, as many people with poor 
fund of knowledge, say). Just see what works has he commented on or 
written himself: commentary on Gita, commentary on 
Visnu-sahasra-nama-stotra (was his first work at all), Bhaja Govindam, 
Damodarastaka, etc. The point is that he generally gave instruction on 
the first aspect of the Absolute Truth, namely Brahman. But he didn't 
reject Paramatma and Bhagavan aspects, as many of his followers did 
because they misunderstood his works as proclaiming existence of only 
Brahman and nothing else.

Sankara knew well about Paramatma and Bhagavan and he has even written 
some words about Them. This is the only reason why Sankaracarya is 
accepted as an acarya (even Srila Prabhupada respected him). But he 
has to correctly understood.

Jahnava Nitai Das:

According to the followers of Sankara, the parampara is as follows:

narayanam padmabhuvam vasistham saktim ca tatputra parasaram ca
vyasam sukam gaudapadam mahantam govindayogindram athasya sisyam |
sri samkaracaryam athasya padmapadam ca hastamalakam ca sisyam
tam totakam varttikakaramanyan asmad gurun santatamanatosmi ||
sadasiva samarambham sankaracarya madhyamam
asmadacarya paryantam vande guru paramparam ||

Narayana, Padmabhuva (Brahma), Vasistha, Sakti, Parasara, Vyasa, Suka, 
Gaudapada, Govinda Bhagavatpada, Sankaracarya, Padmapada, Hastamalaka, 
Totaka, and Suresvara.

