I have to second Master Huifeng's question. The word "sect" needs to be defined, even if loosely. Why?
Vajrayana, Mahayana and Theravada are not sects. That's because they lack the necessary identification in terms of organisation, doctrine and ritual. Buddhism is not like Christianity where most of the churches have a defined organisational structure and a set of beliefs. In fact, there are very few Buddhist groups with an explicit and exclusive teaching, i.e. statements of faith.
Technically speaking, all Buddhists take refuge in the Three Jewels. The monastic community is traditionally defined by the precepts followed, and while there are some minor differences between the three living traditions, they are fairly similar, while the lay community has the same five precepts everywhere. In that sense, there aren't really any sects, we are all followers of the very same Shakyamuni Buddha. (A recommended reading: Sects & Sectarianism: The origins of Buddhist Schools
What defines Pure Land Buddhism? The simple intention to be born in Sukhavati. While the recitation of the name of Amitabha is the most popular form of practice for that, it is not the only one. It doesn't have any unique doctrine, precept, ritual or organisation.
What defines Zen Buddhism? There is nothing that is found in all Zen groups but not outside of Zen. No unique doctrine, precept, ritual or organisation. We could say that Zen has its own lineage system of transmission, but on the one hand there are other Buddhist groups with similar lineages, and on the other there are a number of highly respected Zen teachers without lineage affiliation.
What defines Theravada? That looks somewhat easier, because of the Kathavatthu
, however, if we look at the current state of what is called Theravada, it is something very diverse in their doctrines, practices, rituals and organisations. And since all of them are Theravada, there isn't actually one definitive Theravada school.
What defines Vajrayana? It feels easy to say that all things tantra. However, tantric teachings and practices our found not only in a couple of Tibetan Buddhist groups, but also in Tibetan Bon, in Chinese Buddhism and Taoism, in Japanese Buddhism (mostly Shingon and Tendai, but certain elements exist(ed) in other schools too), and most importantly in various Hindu schools. And if we start limiting the meaning of Vajrayana, we find that there are all sorts of traditions within Buddhism that don't agree with each other on certain points, so like for Theravada, there is no single orthodox school.
So, I think either there aren't really sects in Buddhism, or there are a whole lot of them. Thus some sort of definition is needed to answer the question about the largest Buddhist sect. Or change the question to something else, like "the most popular understanding of enlightenment", "the favourite colour for monastic robes", "the most popular buddha", "the most respected teacher", etc.