Generally any projective group $\mathrm{PGL}(2,\mathbb{F}_q)$ acting on the $q+1$ points of the projective line over $\mathbb{F}_q$ is sharply $3$-transitive. This gives infinitely many $3$-homogeneous but not $4$-homogeneous groups.
A related example I particularly like is the $3$-transitive but $4$-homogeneous group $\mathrm{P}\Gamma\mathrm{L}(2,8)$ obtained by extending $\mathrm{PGL}_2(\mathbb{F}_8)$ by the Frobenius automorphism of order $3$. Such groups are important in the classification of multiplicity-free permutation characters of $S_n$. I have a relevant paper which builds on work of Saxl, and there is also independent work of Godsil and Meagher.
Incidentally, going in the opposite direction, it is not completely obvious that a $k$-homogeneous group on $n$ points is $(k-1)$-homogeneous, provided $k \le n/2$. But this is of course true, and has a neat proof using character theory: the number of orbits of $G \le S_n$ on $k$-subsets is $\langle 1\!\!\uparrow_G^{S_n}, \pi_k \rangle$, where $\pi_k$ is the permutation character of $S_n$ acting on $k$-subsets; now use that $\pi_k - \pi_{k-1}$ is the irreducible character $\chi^{(n-k,k)}$, so the difference has non-negative inner product with any character.