We study $\textit{sparse singular value certificates}$ for random rectangular matrices. If $M$ is an $n \times d$ matrix with independent Gaussian entries, we give a new family of polynomial-time algorithms which can certify upper bounds on the maximum of $\|M u\|$, where $u$ is a unit vector with at most $ηn$ nonzero entries for a given $η\in (0,1)$. This basic algorithmic primitive lies at the heart of a wide range of problems across algorithmic statistics and theoretical computer science. Our algorithms certify a bound which is asymptotically smaller than the naive one, given by the maximum singular value of $M$, for nearly the widest-possible range of $n,d,$ and $η$. Efficiently certifying such a bound for a range of $n,d$ and $η$ which is larger by any polynomial factor than what is achieved by our algorithm would violate lower bounds in the SQ and low-degree polynomials models. Our certification algorithm makes essential use of the Sum-of-Squares hierarchy. To prove the correctness of our algorithm, we develop a new combinatorial connection between the graph matrix approach to analyze random matrices with dependent entries, and the Efron-Stein decomposition of functions of independent random variables. As applications of our certification algorithm, we obtain new efficient algorithms for a wide range of well-studied algorithmic tasks. In algorithmic robust statistics, we obtain new algorithms for robust mean and covariance estimation with tradeoffs between breakdown point and sample complexity, which are nearly matched by SQ and low-degree polynomial lower bounds (that we establish). We also obtain new polynomial-time guarantees for certification of $\ell_1/\ell_2$ distortion of random subspaces of $\mathbb{R}^n$ (also with nearly matching lower bounds), sparse principal component analysis, and certification of the $2\rightarrow p$ norm of a random matrix.