David already gave a nice example showing that you do not get negative trichotomy constructively but it turns out that the situation is more drastic than was obvious to me when I originally encountered this question, so I thought I should write another answer. I'm curious about the status of this question relative to more restrictive notions of constructive ordinal, such as Paul's plump ordinals, but I wasn't able to really make any progress on that question.
I'm going to phrase this in terms of constructive set theory (with power sets and full separation), but something analogous holds in any topos or any type theory with an impredicative $\mathtt{Prop}$. I did not come up with this argument, but I also don't remember where I saw it. Hopefully someone will point out a reference.
As you specified in the comments, an ordinal is a transitive set of transitive sets (and, recall, a binary relation $(R,<)$ is isomorphic to an ordinal $(\alpha,\in)$ iff it is transitive, extensional, and well-founded). Let $0 = \varnothing$, $\Omega = \mathcal{P}(\{0\})$, and $x + 1 = x\cup \{x\}$. Let $1 = 0 + 1 = \{0\}$, $2 = 1 + 1 = \{0,1\}$, etc.
Note that $\mathsf{LEM}$ is equivalent to the statement $\Omega = 2$. Also note that $\Omega$ and $\Omega + 1$ are ordinals.
Proposition. If $\neg \mathsf{LEM}$ holds, then $\Omega +1 \neq 3$ and $\Omega+1$ and $3$ are both $\in$-incomparable and $\subseteq$-incomparable.
Proof. Since $\neg \mathsf{LEM}$, we have that $\Omega \neq 2$. We also clearly have that $\Omega \neq 0$ and $\Omega \neq 1$, so $\Omega \notin 3$. Since $\Omega \in \Omega + 1$, we have that $\Omega + 1 \neq 3$. Since $\Omega \notin 0$, $\Omega \notin 1$, and $\Omega \notin 2$, we have that $\Omega+1$ is not equal to $0$, $1$, or $2$, whereby $\Omega + 1 \notin 3$.
Assume for the sake of contradiction that $3 \in \Omega + 1$. By definition, this means that $3 \in \Omega$ or $3 = \Omega$. $\Omega$ is not $3$ (because $2$ is not a subset of $1 =\{0\}$), but $3$ is also not an element of $\Omega$ (because $3$ is also not a subset of $1$). Therefore $3 \notin \Omega +1$.
Assume for the sake of contradiction that $3 \subseteq \Omega + 1$. This implies that $2 \in \Omega +1$, so either $2 \in \Omega$ or $2 = \Omega$. The second fails because $\neg \mathsf{LEM}$, and the first fails because $2$ is not a subset of $1$. Therefore $3 \not \subseteq \Omega +1$.
Finally, we already know that $\Omega \notin 3$, so is must be that $\Omega + 1 \not \subseteq 3$. $\square$
This implies that in a lot of sheaf toposes (and in the corresponding models of $\mathsf{IZF}$), you don't get negative trichotomy for this definition of ordinal. For instance, $\neg \mathsf{LEM}$ holds in sheaves over Cantor space and the reals. $\neg \mathsf{LEM}$ also holds in the effective topos/realizability model of $\mathsf{IZF}$. Moreover the proposition implies the following:
Corollary. The following are equivalent (where all quantifiers range over ordinals).
- $\neg \neg \forall \alpha \beta (\alpha \in \beta \vee \alpha = \beta \vee \beta \in \alpha)$
- $\neg \neg \forall \alpha \beta (\alpha \subseteq \beta \vee \beta \subseteq \alpha)$
- $\forall \alpha \beta \neg \neg (\alpha \in \beta \vee \alpha = \beta \vee \beta \in \alpha)$
- $\forall \alpha \beta \neg \neg (\alpha \subseteq \beta \vee \beta \subseteq \alpha)$
- $\neg\neg \mathsf{LEM}$
Proof. 5 clearly implies 1 and 2. 1 implies 3 and likewise 2 implies 4 by basic intuitionistic logic. 3 and 4 both imply 1 by instantiating $\alpha = \Omega +1$ and $\beta = 3$. $\square$
That said there are also a decent number of toposes in which $\neg\neg\mathsf{LEM}$ (and therefore negative trichotomy) does hold (assuming a classical world of sets). It holds in finite Kripke frames and therefore (equivalently) in presheaf toposes over finite posetal categories. In particular this means that negative trichotomy does in fact hold in the 'simplest non-classical topos' (i.e., presheaves over $\bullet \to \bullet$).