Yes, they are linearly independent.
Be $B_1,\ldots,B_n$, $B_k=\{v_{k1},\ldots,v_{k|B_k|}\}$, the bases of distinct eigenspaces $V_k$ of $A$, and $\lambda_1,\ldots,\lambda_n$ the corresponding eigenvectors. Obviously $\lambda_i=\lambda_k\iff i=k$, or else the eigenspaces would not be distinct.
Now assume the vectors in $B_1\cup\dots\cup B_n$ were linearly dependent. Then you'd have numbers $\alpha_{kl}$ such that
$$\sum_{k=1}^n\sum_{l=1}^{|B_k|}\alpha_{kl}v_{kl}=0\,. \tag{1}$$
To simplify notation, we define
$$w_k = \sum_{l=1}^{|B_k|}\alpha_{kl}v_{kl}\,.\tag{2}$$
With this the equation $(1)$ simplifies to
$$\sum_{k=1}^n w_k = 0\,.$$
Obviously $w_k\in V_k$. Therefore we get
$$A\sum_{k=1}^n w_k = \sum_{k=1}^n \lambda_k w_k=0\,. \tag{3}$$
Now we consider two cases for $\lambda_n$. The first case is that $\lambda_n=0$. Then obviously in equation $(3)$ the term $k=n$ vanishes and therefore can be omitted. That is, in that case, $B_1\cup\dots\cup B_{n-1}$ is already linearly dependent.
Now consider $\lambda_n\ne 0$. Then we can divide $(3)$ by $\lambda_n$ and subtract $(2)$ to obtain
$$\sum_{k=1}^n\left(\frac{\lambda_k}{\lambda_n}-1\right)w_k = 0\,.$$
Again, we see that the coefficient of $w_n$ vanishes, therefore already $B_1\cup\dots\cup B_n$ is linearly dependent.
So we have shown that if the basis vectors of a set of eigenspaces are linearly dependent, then we can remove one of the eigenspaces and still have a linearly dependent set. But we can do the same step with the new set, until we arrive at just one eigenspace, for which we again have to conclude linear dependence. But we chose a basis for the eigenspace, so that cannot be linearly dependent. Therefore our original assumption must have been wrong, and $B_1\cup\dots\cup B_n$ indeed is linearly independent.