If we're talking about actual ships, USS Constitution is tiny compared to most US Navy ships ;)

(Not sure how good this example is, but anyway - flagship doesn't have to be physically giant.)

It would probably be useful to read the whole article that one links to, because there's no flagship small enough to fit in your pocket, unless...:

https://en.wikipedia.org/wiki/Flagship#Flagship_as_metaphor

Now, whether an iPhone Mini fits into that metaphor can be debated, but it's just a metaphor, after all. :-)